X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details sodium malonate, Tris, 2-mercaptoethanol, EDTA, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 154.41 α = 90
b = 154.41 β = 90
c = 154.41 γ = 90
Symmetry
Space Group P 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2001-04-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.97 SSRL BL9-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.2 20 99.9 0.064 -- -- 6.7 32543 32513 0.0 0.0 28.1
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.2 2.24 99.8 0.596 -- 2.13 -- 1585

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 2.2 19.77 0.0 0.0 32543 32418 1691 99.8 -- -- 0.248 0.273 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2 2.34 -- 262 5035 0.277 0.304 0.019 99.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 40.2
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 1.27
c_scbond_it 1.93
c_bond_d 0.006
c_scangle_it 2.84
c_angle_deg 1.2
c_improper_angle_d 0.72
c_dihedral_angle_d 22.8
c_mcangle_it 2.15
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2685
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 145

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing